If the Arks were around before ME3 then no matter what they do it's going to feel forced. No one but Hackett and Anderson believed Shepard about the Reapers, and there is no way they would of had the clout to make the Arks and convince people of every race to get on them, nor would they have wasted the COLOSSAL resources required when they could of put it towards putting more stuff together for the Reapers. You know. Like dreadnoughts. Thannix cannons. Carriers. Any of those things would of flown with the Alliance Brass (especially given escalating hostility with the Batarians), while I can't see the Arks doing that. We've only been on the Galactic scene for less than thirty years, I can't see the novelty having worn off on humanity so quickly as to warrant wanting to go to Andromeda, and that's the only other motive people could have in that time frame, because no one was taking the Reaper threat seriously.
I mean, they COULD go that route, but like I said, there's no way it's ever going to read as anything other than being incredibly ham-fisted.
On Mars, the Protheans left a treasure trove of deus ex machinas. So even before ME1 they found the Ark designs way back when, but hit a dead end. Then after ME1 Hackett got the program up and running again and the Alliance got the aid of the top asari, salarian and turian engineers to work on the project in secret. I'm sure Liara, being so important, found something in the Archives while Shep was in jail and that was the final icing on the cake. Of course everyone keeps this from Shepard because reasons. The Council secretly gets volunteers from all the races. Bioware will ignore the individual issues with certain races that will make this untenable because F the lore. Ark takes off before ME3 starts. And they won't have a quantum entanglement communicator because of some pseudo-science space magic bs about Reaper possibly being able to track their location via the entangled particle left behind in the milky way. So no way to communicate with the Milky Way and know what happened. Or they'll just be lazy and act like QEC don't exist. Maybe this is give them an excuse to throw protheans in Andromeda as with the Crucible we're just following in their footsteps.
What's your prediction, folks?